After being released from Aberdeen's youth set-up, McAllister was given a chance to resurrect his career at Inverness Caledonian Thistle. In three seasons he played in over 50 games, but scored just five goals. He made his league début for Inverness on 30 April 2005, as a second-half substitute against Kilmarnock. His first goal came in a Scottish Cup tie against Ayr United on 7 January 2006. After failing to build upon his early potential, first team appearances at Inverness became scarce. He was loaned out to Second Division club Peterhead in January 2008. He played four times for the club and scored one goal, in a 9–2 victory against Berwick Rangers. In April 2008, McAllister signed a new one-year contract with Inverness, however on 24 January 2009, he left the club by mutual consent.
Having initially said he wanted to return to full-time football, McAllister then dropped down to the Third Division to join relegated Peterhead to be closer to Aberdeen to get an apprenticeship in plumbing, in order to have a career to fall back on when he retired from football. On 20 April 2013, he scored the winning goal as Peterhead won 2–1 against Rangers at Ibrox. On 8 April 2014, McAllister was awarded the SPFL Player of the month for March 2014, after scoring eight goals in six games during the month, becoming the first player from outside the Scottish Premiership to win the award. On 12 April 2014, McAllister scored Peterhead's second goal in a 2–0 win against Clyde, a result which meant the club won the Scottish League Two title and promotion to League One. On 27 April 2014, McAllister was named as PFA Scotland League Two Player of the Year for 2013–14. He signed a new contract on 11 August 2014, keeping him at Peterhead until 2017. In an interview in 2015, McAllister said he could not see himself leaving Peterhead for the rest of his career. On 18 August 2015, he scored all five of his side's goals in a 2015–16 Scottish Challenge Cup match against Falkirk. Peterhead went all the way to the final at Hampden Park, losing 4–0 to Rangers. In August 2016, McAllister signed a new two-year deal with Peterhead to run to the end of the 2017–18 season after rejecting the opportunity to join Dundee United. McAllister scored five goals in a match again in October 2017, this time against more modest opposition, in a 9–0 victory over amateurs Colville Park in the 2017–18 Scottish Cup. By January 2018 he had 24 goals in 24 matches during the season, making him the nation's leading scorer alongside Alan Trouten of Albion Rovers. After scoring against Albion Rovers in August 2018, McAllister became the first player to reach 100 goals since the SPFL began operation in 2013.
Cove Rangers
In January 2020, after handing in a transfer request to Peterhead, McAllister moved to League Two side Cove Rangers on a three-and-a-half year deal for an undisclosed fee.
